release prep for v0.13.0

gerlichlab · Feb 19, 2025 · 834388d · 834388d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,14 +4,18 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project will adhere to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [v0.13.0] - Unreleased
+## [v0.14.0] - Unreleased
 
 ### Added
-* Discard detected beads which are in nuclear regions. See [Issue 401](https://github.com/gerlichlab/looptrace/issues/400) and [Issue 403](https://github.com/gerlichlab/looptrace/issues/403). 
-This is designed to prevent accidentally using a FISH spot as a bead, which is especially likely when doing single-channel tracing, in which beads and FISH signal are captured at the same wavelength.
 * Add a proximity filter between beads and FISH spots. In other words, discard any "FISH spot" which is too close to a bead. Again, this is related to the idea of mixing up the two, especially during single-channel tracing. 
 See [Issue 400](https://github.com/gerlichlab/looptrace/issues/400) and [Issue 403](https://github.com/gerlichlab/looptrace/issues/403).
 
+## [v0.13.0] - 2025-02-19
+
+### Added
+* Discard detected beads which are in nuclear regions. See [Issue 401](https://github.com/gerlichlab/looptrace/issues/400) and [Issue 403](https://github.com/gerlichlab/looptrace/issues/403). 
+This is designed to prevent accidentally using a FISH spot as a bead, which is especially likely when doing single-channel tracing, in which beads and FISH signal are captured at the same wavelength.
+
 ## [v0.12.1] - 2025-02-19
 
 ### Fixed

diff --git a/Dockerfile b/Dockerfile
@@ -15,7 +15,7 @@ RUN apt-get update -y && \
 RUN mkdir /looptrace
 WORKDIR /looptrace
 COPY . /looptrace
-RUN mv /looptrace/target/scala-3.5.2/looptrace-assembly-0.13.0-SNAPSHOT.jar /looptrace/looptrace
+RUN mv /looptrace/target/scala-3.5.2/looptrace-assembly-0.13.0.jar /looptrace/looptrace
 
 # Install new-ish R and necessary packages.
 RUN echo "Installing R..." && \

diff --git a/build.sbt b/build.sbt
@@ -8,7 +8,7 @@ val primaryJavaVersion = "11"
 val primaryOs = "ubuntu-latest"
 val isPrimaryOsAndPrimaryJavaTest = s"runner.os == '$primaryOs' && runner.java-version == '$primaryJavaVersion'"
 ThisBuild / scalaVersion     := "3.5.2"
-ThisBuild / version          := "0.13.0-SNAPSHOT"
+ThisBuild / version          := "0.13.0"
 ThisBuild / organization     := orgName
 ThisBuild / organizationName := "Gerlich Group, IMBA, OEAW"
 

diff --git a/looptrace/__init__.py b/looptrace/__init__.py
@@ -22,7 +22,7 @@
 
 
 # This is put into place by the docker build, as declared in the Dockerfile.
-LOOPTRACE_JAR_PATH = importlib.resources.files(__name__).joinpath("looptrace-assembly-0.13.0-SNAPSHOT.jar")
+LOOPTRACE_JAR_PATH = importlib.resources.files(__name__).joinpath("looptrace-assembly-0.13.0.jar")
 LOOPTRACE_JAVA_PACKAGE = "at.ac.oeaw.imba.gerlich.looptrace"
 
 FIELD_OF_VIEW_COLUMN = "fieldOfView"

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "looptrace"
-version = "0.13.0rc1"
+version = "0.13.0"
 description = "Library and programs for tracing chromatin loops from microscopy images"
 authors = [
     "Kai Sandvold Beckwith",